In a statement issued after the events, Mr Pyne said he left the chamber "to negate the tainted vote of the Member for Dobell".

"The Coalition has taken the principled stand of refusing to accept his vote under any circumstances," the statement said.

Mr Abbott later told reporters that he believed the affair was "obviously a stunt orchestrated by Craig Thomson, Anthony Albanese and the Government."

"As soon as it became apparent that the Government was pulling this stunt, Christopher Pyne and I absented ourselves from the chamber. So we did not accept the tainted vote of Craig Thomson," he said.

"We did exactly the same thing with Craig Thomson that the former government did with Mal Colston."

Mr Thomson denied the accusation, saying he had not consulted anyone in Labor before the vote.

Instead, he accused the Opposition of pulling stunts with motions to suspend standing orders.

Independent MP Andrew Wilkie is unimpressed by the whole affair.

"I thought that was quite an unedifying spectacle," he said.

"Craig Thomson has the right to sit in the chamber and to represent the people of Dobell. And for the parties... to be scheming in ways to make his vote not count, I think is to actually treat Craig Thomson's fundamental right in accordance with the constitution."